Skewed X-chromosome inactivation in unsolved neurodevelopmental disease cases can guide re-evaluation For X-linked genes

Abstract

Despite major technical and genetic advances, more than half of the neurodevelopmental disorders (NDDs) cases remain undiagnosed.We explored the frequency of non-random XCI in the mothers of male patients and in affected females from a clinically heterogeneous cohort of unsolved NDD cases, negative at FRAXA, chromosomal microarray analysis and Trio Exome Sequencing. We hypothesize that an unbalanced XCI could unmask previously discarded genetic variants on the X chromosome connected both to XCI and NDD.A multiplex uorescent-PCR-based assay was used to screen the XCI pattern after methylation sensitive HhaI digestion. Trio-based ES re-analysis was performed in families with skewed XCI occurrence. Linkage analysis and RT-PCR were used to further study the X-chromosome inactive allele. X-drop was used to de ne the chromosome deletion boundaries.We found a skewed XCI (>90%) in 16/186 mothers of affected NDD males (8.6%) and 12/90 female patients (13.3%), far beyond the expected XCI in normal population (3.6%, OR=4.10; OR=2.51). Reanalyzing ES and clinical data, we solved 7/28 cases (25%). These included variants in the KDM5C, PDZD4, PHF6, TAF1, OTUD5, and ZMYM3, and a genomic deletion spanning exons 3-4 of the ATRX gene.The identi cation of a skewed XCI is an easy assay that can help selecting a subgroup of patients for the re-evaluation of X-linked variants, improving the diagnostic yield in NDD patients, and allowing the identi cation of new X-linked disorders.

Enigma of the Developmental Causes in Individuals with Autism Spectrum Disorder (ASD)

“…A different study conducted in 2023, much like the 2003 study, found that doing more profiling and research into X chromosomes may help in identifying the causes of neurodivergent disorders and identifying other X-linked disorders. [10] This study suggests that there's an age and disorder-specific pattern in how a brain develops and changes which cause autism, although this study does not confirm whether it's specific to ASD or present in other neurodevelopmental disorders, even though that would be consistent with previous research.…”

“…[3] The study interestingly looked at Head Circumference (HC) at birth to be an early indicator of autism. [10] The first phase at birth showed that the average HC measurement is at the 25th percentile but was not accompanied by a decrease in prenatal body growth as the body length and weight at birth are not less than the values of healthy infants at birth. The study also found that brain volume decreases at birth appeared to be small and could not be used as a pre-onset indicator of autism in later years.…”

DNA methylation analysis in patients with neurodevelopmental disorders improves variant interpretation and reveals complexity

“…The patients were divided into three categories (see Tables 1 and S1 ): (1a) validation cohort #1a, which consisted of 34 NDD cases with pathogenic or likely pathogenic single nucleotide variants (SNVs) in a gene with known disease-specific methylation patterns or episignatures that are listed in the EpiSign v.3 classifier; (1b) validation cohort #1b, which consisted of 25 NDD cases with pathogenic or likely pathogenic CNVs that are also listed in the EpiSign v.3 classifier; (2) an uncertain cohort composed of 18 NDD cases with an SNV/CNV VUS or with a strong clinical suspicion but no specific variant identified, and (3) 20 unresolved NDD cases defined by females or mothers of unresolved male cases that showed skewed X chromosome inactivation (XCI) of more than 80% (Supplemental Materials and methods). 17 …”

Stochasticity in genetics and gene regulation

“…Such a situation has also been described for females with Duchenne muscular dystrophy [ 25 , 26 ]. Studying X-inactivation patterns in ID families with affected and unaffected female family members with XCI skewing in opposite directions, and often with affected males in the kindred, may identify variants whose causative nature was not initially recognized because it was also found in unaffected females [ 30 ].…”